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Research: Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
- Wouter Steyaert,
- Lydia Sagath,
- German Demidov,
- Vicente A. Yépez,
- Anna Esteve-Codina,
- Julien Gagneur,
- Kornelia Ellwanger,
- Ronny Derks,
- Marjan Weiss,
- Amber den Ouden,
- Simone van den Heuvel,
- Hilde Swinkels,
- Nick Zomer,
- Marloes Steehouwer,
- Luke O'Gorman,
- Galuh Astuti,
- Kornelia Neveling,
- Rebecca Schüle,
- Jishu Xu,
- Matthis Synofzik,
- Danique Beijer,
- Holger Hengel,
- Ludger Schöls,
- Kristl G. Claeys,
- Jonathan Baets,
- Liedewei Van de Vondel,
- Alessandra Ferlini,
- Rita Selvatici,
- Heba Morsy,
- Marwa Saeed Abd Elmaksoud,
- Volker Straub,
- Juliane Müller,
- Veronica Pini,
- Luke Perry,
- Anna Sarkozy,
- Irina Zaharieva,
- Francesco Muntoni,
- Enrico Bugiardini,
- Kiran Polavarapu,
- Rita Horvath,
- Evan Reid,
- Hanns Lochmüller,
- Marco Spinazzi,
- Marco Savarese,
- Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
- Leslie Matalonga,
- Steven Laurie,
- Han G. Brunner,
- Holm Graessner,
- Sergi Beltran,
- Stephan Ossowski,
- Lisenka E.L.M. Vissers,
- Christian Gilissen,
- Alexander Hoischen,
- and on behalf of the Solve-RD consortium
Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
...program that aims to identify disease-causing genetic variants in previously undiagnosed RD families. We utilized 10-fold coverage HiFi long-read sequencing (LRS) for detecting causative structural variants (SVs), single-nucleotide variants (SNVs), insertion-deletions (indels), and short tandem repeat...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...importance, our understanding of how SMs originate and at which rates remains limited. Long-read sequencing is a relatively new technology for improving SM discovery (Hollox et al. 2022), and its application promises a more comprehensive description of the spectrum of new mutations. For example, Pacific...
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Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
- Giulia F. Del Gobbo and
- Kym M. Boycott
Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
...variantsSVs, genomic alterations >50 bp in size including insertions, deletions, duplications, inversions, translocations, and CGRs, account for the largest amount of sequence variation between individual s (Sudmant et al. 2015b; Chaisson et al. 2019) and are thus crucial to comprehensively assess in RD...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...multiple family members at high rates (Paskov et al. 2021). Large structural variants such as deletions and duplications may also hinder attempts to identify crossovers in families by producing genomic regions with unusual, non-Mendelian variant patterns (Roach et al. 2010).Several approaches have been...
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Method: A machine-learning approach for accurate detection of copy number variants from exome sequencing
- Vijay Kumar Pounraja,
- Gopal Jayakar,
- Matthew Jensen,
- Neil Kelkar,
- and Santhosh Girirajan
Genome Res. July 2019 29: 1134-1143; Published in Advance June 6, 2019, doi:10.1101/gr.245928.118
...the utility of CN-Learn. Our study also serves as a proof-of-principle for future studies that could utilize CN-Learn with “gold standard” CNVs curated from multiple genomic technologies, such as Pacific Biosciences (PacBio) SMRT sequencing (John et al. 2009), Illumina long-read sequencing (Voskoboynik et al...
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Method: Polishing copy number variant calls on exome sequencing data via deep learning
- Furkan Özden,
- Can Alkan,
- and A. Ercüment Çiçek
Genome Res. June 2022 32: 1170-1182; Published in Advance June 13, 2022, doi:10.1101/gr.274845.120
...set contains the WGS-based CNV calls of nine s selected from the 1000 Genomes Project samples, for which a consensus call set was obtained using 15 different WGS-based CNV callers with comparisons against high-quality SVs generated using long-read Pacific Biosciences (PacBio) data with a single...
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Commentary: Implications of the first complete human genome assembly Genome Res. April 2022 32: 595-598; Published in Advance March 31, 2022, doi:10.1101/gr.276723.122

...in a genomics era. The new T2T-CHM13 represents a significant advancement in this effort, leveraging improvements in long-read sequencing technologies to resolve some of the most recalcitrant loci (centromeres!), identify new genes, reduce artifacts, and eliminate false variant calls across previously collapsed...
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Research: Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes
- Alexandra J. Scott,
- Colby Chiang,
- and Ira M. Hall
Genome Res. December 2021 31: 2249-2257; Published in Advance September 20, 2021, doi:10.1101/gr.275488.121
...estimated that a large number of rare noncoding deletions—an average of 19.1 per individual—appear to be under strong purifying selection (Abel et al. 2020). Furthermore, the burden of de novo CNVs has been associated with autism spectrum disorder, including for noncoding variants (Turner et al. 2017...
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Method: Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair
- Ryan J. McGinty,
- Rachel G. Rubinstein,
- Alexander J. Neil,
- Margaret Dominska,
- Denis Kiktev,
- Thomas D. Petes,
- and Sergei M. Mirkin
Genome Res. December 2017 27: 2072-2082; Published in Advance November 7, 2017, doi:10.1101/gr.228148.117
.... Interrogating the “unsequenceable” genomic trinucleotide repeat disorders by long-read sequencing. Genome Med 9: 65. ↵Loman NJ, Quick J, Simpson JT. 2015. A complete bacterial assembled de novo using only nanopore sequencing data. Nat Methods 12: 733–735. ↵Macintyre G, Ylstra B, Brenton JD. 2016. Sequencing...
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Method: Read clouds uncover variation in complex regions of the human genome
- Alex Bishara,
- Yuling Liu,
- Ziming Weng,
- Dorna Kashef-Haghighi,
- Daniel E. Newburger,
- Robert West,
- Arend Sidow,
- and Serafim Batzoglou
Genome Res. October 2015 25: 1570-1580; Published in Advance August 18, 2015, doi:10.1101/gr.191189.115
...a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive...
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